From 82e4b484fce1cc9996482374f175673f5b25473f Mon Sep 17 00:00:00 2001
From: James Richard Otieno <james.otieno@theiagen.com>
Date: Wed, 20 Sep 2023 12:01:53 -0400
Subject: [PATCH] adding bed file input (#190)

---
 workflows/phylogenetics/wf_snippy_tree.wdl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/workflows/phylogenetics/wf_snippy_tree.wdl b/workflows/phylogenetics/wf_snippy_tree.wdl
index 2b5aec4be..3d8f7671a 100644
--- a/workflows/phylogenetics/wf_snippy_tree.wdl
+++ b/workflows/phylogenetics/wf_snippy_tree.wdl
@@ -31,6 +31,7 @@ workflow snippy_tree_wf {
     Int? snippy_core_cpu 
     Int? snippy_core_disk_size
     Int? snippy_core_memory
+    File? snippy_core_bed
     
     Int? gubbins_disk_size
     Int? gubbins_memory
@@ -61,7 +62,8 @@ workflow snippy_tree_wf {
       docker = snippy_core_docker,
       cpu = snippy_core_cpu,
       disk_size = snippy_core_disk_size,
-      memory = snippy_core_memory
+      memory = snippy_core_memory,
+      bed_file = snippy_core_bed
   }
   if (use_gubbins) {
     call gubbins_task.gubbins {